User: user230613

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user230613280
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Europe
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1 year, 3 months ago
Joined:
5 years, 4 months ago
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Posts by user230613

<prev • 62 results • page 1 of 7 • next >
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Comment: C: Difference between the Fasta files from UCSC and Gencode/Ensembl
... Hello Denise, According to you answer, can I use then as reference genome the one located here: `ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz` ; and use the annotation files pr ...
written 23 months ago by user230613280
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Mate negative strand flag does not match read negative strand flag of mate
... I get this error when running **picard ValidateSamFile** in a RNA-Seq bam file produced by **hisat2**: ERROR: Record 52, Read name K00103:277:HL7HMBBXX:6:2109:23551:26054, Mate negative strand flag does not match read negative strand flag of mate This is the read in the bam file: `samtools v ...
rnaseq bam validatesamfile written 2.1 years ago by user230613280 • updated 2.1 years ago by Santosh Anand5.0k
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Comment: C: TPM VS FPKM VS TMM and K-mer specific expression quantification
... Hello, again, I wonder if you could guide a little bit with my previous question? Thank you :) ...
written 2.2 years ago by user230613280
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Comment: C: TPM VS FPKM VS TMM and K-mer specific expression quantification
... Hi Rob. Could you guide me a bit? If I want to find the expression of a given kmer (10nt) that is common between two transcripts, should I add the TPMs of both transcripts? ...
written 2.4 years ago by user230613280
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GATK; Variant calling RNA-Seq best practices: bam processing steps
... Hi folks, I have been looking for the best approach for call the variants in RNA-Seq data. GATK proposes the following workflow: > 1) Map the reads using STAR. > > 2) Remove duplicates > > 3) Split N Trim > > 4) Indel realignment > > 5) Base recalibration > & ...
gatk variant_calling rna-seq written 2.4 years ago by user230613280 • updated 2.4 years ago by andrew.j.skelton735.9k
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Comment: C: Specific sequence abundance using RNA-Seq
... @Brian, I want to measure the expression of that sequence using RNA-Seq data, I don't want to extract the Kmer sequence from my reads. ...
written 2.7 years ago by user230613280
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Specific sequence abundance using RNA-Seq
... Hi, I would like to measure the expression, the abundance, of a given sequence, a specific 9-mer. I have `RNA-Seq` data. I know that the 9-mer is not unique in the genome, is not private of a specific gene. It is present in more than one isoform of gene A and also is present in gene B. How can I ge ...
expression rna-seq written 2.7 years ago by user230613280 • updated 2.7 years ago by Brian Bushnell17k
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Comment: C: What Ngs Read Simulators Are Available For Paired-End Data?
... Thank you for the fast answer. I'll try the bedtools pre-step. Another issue.. I've realised that in PE mode, the names of the output reads in the two files are not paired, is there any option for this? ...
written 2.7 years ago by user230613280
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Comment: C: What Ngs Read Simulators Are Available For Paired-End Data?
... Hi Brian! Is it possible to generate reads in specific intervals? WES-like read simulation? ...
written 2.7 years ago by user230613280
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Comment: C: Subset of transcripts - Do I need to re-scale the TPM values?
... Mmmm.. that's true, but I'm not interested in the non-coding transcripts at all. That's why I have posted a second question "Is there a difference between this approach or running Kallisto only on those coding transcripts?", because if you use only coding set of transcripts when running kallisto, th ...
written 2.7 years ago by user230613280

Latest awards to user230613

Popular Question 16 months ago, created a question with more than 1,000 views. For Samtools: variant calling for INDELs
Great Question 22 months ago, created a question with more than 5,000 views. For Trinity strand specific: RF or FR
Great Question 22 months ago, created a question with more than 5,000 views. For Extract reads within given region, and their mates
Popular Question 22 months ago, created a question with more than 1,000 views. For Samtools: variant calling for INDELs
Popular Question 22 months ago, created a question with more than 1,000 views. For promoter position estimation
Popular Question 22 months ago, created a question with more than 1,000 views. For ggheatmap R script error.
Popular Question 22 months ago, created a question with more than 1,000 views. For Intersect multiple bed and keep all fields
Popular Question 23 months ago, created a question with more than 1,000 views. For Samtools: variant calling for INDELs
Popular Question 23 months ago, created a question with more than 1,000 views. For promoter position estimation
Popular Question 2.1 years ago, created a question with more than 1,000 views. For promoter position estimation
Popular Question 2.1 years ago, created a question with more than 1,000 views. For CIRCOS plot with Chip-Seq Data
Popular Question 2.3 years ago, created a question with more than 1,000 views. For promoter position estimation
Popular Question 2.7 years ago, created a question with more than 1,000 views. For promoter position estimation
Popular Question 2.7 years ago, created a question with more than 1,000 views. For CIRCOS plot with Chip-Seq Data
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Intersect multiple bed and keep all fields
Student 2.8 years ago, asked a question with at least 3 up-votes. For Extract reads within given region, and their mates
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Trinity strand specific: RF or FR
Popular Question 3.3 years ago, created a question with more than 1,000 views. For Trinity strand specific: RF or FR
Popular Question 3.3 years ago, created a question with more than 1,000 views. For Intersect multiple bed and keep all fields
Popular Question 3.7 years ago, created a question with more than 1,000 views. For Trinity strand specific: RF or FR
Popular Question 3.7 years ago, created a question with more than 1,000 views. For Extract sequence number "X" from multifasta file
Popular Question 3.7 years ago, created a question with more than 1,000 views. For Extract reads within given region, and their mates
Supporter 4.9 years ago, voted at least 25 times.

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